Comparison of Statistical Approaches for the Analysis of Proteome Expression Data of Differentiating Neural Stem Cells

Maurer, Martin H.; Feldmann, Robert; Brömme, J.O.; Kalenka, Armin

doi:10.1021/pr049841l

Cited by 50 publications

(34 citation statements)

References 16 publications

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“…Different kinds of results may be generated depending on the statistical tools made available by the different programs for 2-DE analysis (Maurer et al 2005;Meunier et al 2005).…”

Section: Discussionmentioning

confidence: 99%

Operator- and software-related post-experimental variability and source of error in 2-DE analysis

et al. 2011

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In the field of proteomics, several approaches have been developed for separating proteins and analyzing their differential relative abundance. One of the oldest, yet still widely used, is 2-DE. Despite the continuous advance of new methods, which are less demanding from a technical standpoint, 2-DE is still compelling and has a lot of potential for improvement. The overall variability which affects 2-DE includes biological, experimental, and post-experimental (software-related) variance. It is important to highlight how much of the total variability of this technique is due to post-experimental variability, which, so far, has been largely neglected. In this short review, we have focused on this topic and explained that post-experimental variability and source of error can be further divided into those which are software-dependent and those which are operator-dependent. We discuss these issues in detail, offering suggestions for reducing errors that may affect the quality of results, summarizing the advantages and drawbacks of each approach.

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“…Different kinds of results may be generated depending on the statistical tools made available by the different programs for 2-DE analysis (Maurer et al 2005;Meunier et al 2005).…”

Section: Discussionmentioning

confidence: 99%

Operator- and software-related post-experimental variability and source of error in 2-DE analysis

et al. 2011

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“…In simple cases, with only two groups, this reduces to a Student's t-test, whereas in more complicated designs, such as ours, an ANOVA is used. Univariate analysis appears to be appropriate for the detection of proteomic changes when the expression occur in isolation with respect to other proteins of the gel [25], even though applying different univariate statistical methods can produce divergent groups of significant spots when applied to the same dataset [26].…”

Section: Discussionmentioning

confidence: 99%

Serum proteomic analysis during nicotine self‐administration, extinction and relapse in rats

et al. 2008

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Nicotine dependence is known to induce long-term neural adaptations in brain. The purpose of this study was to verify whether specific protein patterns related to nicotine self-administration states could also be detected in a peripheral tissue. A serum proteomic analysis was performed by 2-DE on samples taken at six time points: N, naïve; P, priming; S, self-administration; W, withdrawal; E, extinction; R, relapse. After image analysis, spot volume values were submitted to a principal component analysis and relevant comparisons were selected. In N versus S; S versus W; E versus R; S versus R and S versus E comparisons a clear separation between groups could be observed, suggesting that each self-administration state correlates with a specific protein expression pattern. Partial least squares discriminant analysis was adopted to rank proteins by the contribution to the overall separation. A number of spots were identified; among them, C reactive protein and haemopexin displayed a significant reduction after nicotine administration; two haemopexin isoforms were decreased in the S state and antithrombin III was increased in the E phase. This study showed that specific protein patterns related to the nicotine self-administration states exist in serum. Further development of this approach may provide biomarkers to assess dependence states of drug-taking individuals.

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“…Only proteins that are considered significantly different by Student's t-test were subjected to in-gel trypsin digestion and subsequent proteomic analyses. This is the normal procedure for proteomics studies, as sophisticated statistical analysis used for microarray studies are not applicable for proteomics studies [75].…”

Section: Statisticsmentioning

confidence: 99%

Proteomic identification of brain proteins in the canine model of human aging following a long-term treatment with antioxidants and a program of behavioral enrichment: Relevance to Alzheimer's disease

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Joshi

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et al. 2008

Neurobiology of Aging

173

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Aging and age-related disorders such as Alzheimer's disease (AD) are usually accompanied by oxidative stress as one of the main mechanisms contributing to neurodegeneration and cognitive decline. Aging canines develop cognitive dysfunction and neuropathology similar to those seen in humans, and the use of antioxidants results in reductions in oxidative damage and in improvement in cognitive function in this canine model of human aging. In the present study, the effect of a longterm treatment with an antioxidant fortified diet and a program of behavioral enrichment on oxidative damage was studied in aged canines. To identify the neurobiological mechanisms underlying these treatment effects, the parietal cortex from 23 beagle dogs (8.1-12.4 years) were treated for 2.8 years in one of four treatment groups: i.e., control food-control behavioral enrichment (CC); control food -behavioral enrichment (CE); antioxidant food-control behavioral enrichment (CA); and enriched environment -antioxidant fortified food (EA). We analyzed the levels of the oxidative stress biomarkers, i.e., protein carbonyls, 3-nitrotyroine (3NT), and the lipid peroxidation product, 4- Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access Author ManuscriptNeurobiol Aging. Author manuscript; available in PMC 2009 January 1. Published in final edited form as:Neurobiol Aging. 2008 January ; 29(1): 51-70. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript hydroxynonenal (HNE), and observed a decrease in their levels on all treatments when compared to control, with the most significant effects found in the combined treatment, EA. Since EA treatment was most effective, we also carried out a comparative proteomics study to identify specific brain proteins that were differentially expressed and used a parallel redox proteomics approach to identify specific brain proteins that were less oxidized following EA. The specific protein carbonyl levels of glutamate dehydrogenase [NAD (P)], glyceraldehyde-3-phosphate dehydrogenase (GAPDH), α-enolase, neurofilament triplet L protein, glutathione S-transferase (GST) and fascin actin bundling protein were significantly reduced in brain of EA-treated dogs compared to control. We also observed significant increases in expression of Cu/Zn superoxide dismutase, fructose-bisphosphate aldolase C, creatine kinase, glutamate dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase. The increased expression of these proteins and in particular Cu/Zn SOD correlated with improved cognitive function. In addition, there was a significant increas...

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Comparison of Statistical Approaches for the Analysis of Proteome Expression Data of Differentiating Neural Stem Cells

Cited by 50 publications

References 16 publications

Operator- and software-related post-experimental variability and source of error in 2-DE analysis

Operator- and software-related post-experimental variability and source of error in 2-DE analysis

Serum proteomic analysis during nicotine self‐administration, extinction and relapse in rats

Proteomic identification of brain proteins in the canine model of human aging following a long-term treatment with antioxidants and a program of behavioral enrichment: Relevance to Alzheimer's disease

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